GSM6893371: Collagen-induced arthritis (CIA), scRNA-seq; Mus musculus; RNA-Seq
GemCode Single Cell platform (10X genomics) was used to determine the transcriptome of single cells. A single-cell suspension was obtained from the flushed bone marrow mixture of the mice femur (n = 3 mice from each sample group (CIA, CIA treated, and DBA control)) and subjected to Ficoll gradient centrifugation to enrich for mononuclear cells . Samples were profiled based on viability and amount and a range of 81-85% viability was achieved. A total of 10,000 cells were recorded for each run, followed by GEM-RT and cDNA amplification. Single-cell library preparation was performed by the Johns Hopkins School of Medicine for Genomics and Bioinformatics (Core facility) and the quality of cDNA samples was examined by an Agilent 2100 Expert High Sensitivity DNA Assay. Single-cell libraries were constructed by attaching P5 and P7 primer sites and sample indices to the cDNA. ScRNA-seq was performed on the Illumina NovaSeq 6000 S2 Flow Cell according to the manufacturer's protocol to a depth ranging from 315 to 377 million reads per sample.